Using Multisplit for sing cell

[shyam_u2]

Hi,

I have a complex morphological cell which takes a longer tome to run. So i wanted to use multi split method of parallelization. I was going through this post which was very informative.

http://www.neuron.yale.edu/phpBB/viewtopic.php?t=2018

So i followed the steps which was mentioned by Ted. However when i execute mpiexec -np 4 nrniv -mpi -NSTACK 2000 -c model=4 init.hoc it gives me the following error

c = 32642 maxfactor = 0.3 cm = 2448.15
total complexity is 32719
1 cells
25 pieces
maximum complexity is 8508.6 for host 3
load imbalance is 4.0%
maximum of 7 pieces on host 2
at least one cell is broken into 25 pieces (bilist[0], gid 0)
at least one cell has 15 sids (bilist[0], gid 0)
nrniv(14384) malloc: *** error for object 0x10a5a8ec0: incorrect checksum for freed object - object was probably modified after being freed.
*** set a breakpoint in malloc_error_break to debug
[golgi:14384] *** Process received signal ***
[golgi:14384] Signal: Abort trap (6)
[golgi:14384] Signal code: (0)
[golgi:14384] [ 0] 2 libSystem.B.dylib 0x00007fff8454c67a _sigtramp + 26
[golgi:14384] [ 1] 3 ??? 0x0000000000000001 0x0 + 1
[golgi:14384] [ 2] 4 libSystem.B.dylib 0x00007fff845c9901 szone_error + 519
[golgi:14384] [ 3] 5 libSystem.B.dylib 0x00007fff844f5c83 tiny_free_list_remove_ptr + 251
[golgi:14384] [ 4] 6 libSystem.B.dylib 0x00007fff844f2e9a szone_free_definite_size + 1153
[golgi:14384] [ 5] 7 libnrniv.0.dylib 0x00000001003c41c6 _ZN17MultiSplitControl14exchange_setupEv + 5942
[golgi:14384] [ 6] 8 libnrniv.0.dylib 0x00000001003c5966 _ZN17MultiSplitControl10multisplitEdii + 886
[golgi:14384] [ 7] 9 libnrniv.0.dylib 0x00000001003999e2 _ZL10multisplitPv + 98
[golgi:14384] [ 8] 10 libnrnoc.0.dylib 0x0000000100196b2c call_ob_proc + 636
[golgi:14384] [ 9] 11 libnrnoc.0.dylib 0x00000001001982b5 hoc_object_component + 1141
[golgi:14384] [10] 12 libnrnoc.0.dylib 0x000000010018f306 hoc_execute + 86
[golgi:14384] [11] 13 liboc.0.dylib 0x00000001001ed311 hoc_run1 + 81
[golgi:14384] [12] 14 liboc.0.dylib 0x00000001001ee3d7 hoc_main1 + 183
[golgi:14384] [13] 15 nrniv 0x0000000100002122 ivocmain + 898
[golgi:14384] [14] 16 nrniv 0x0000000100001bae main + 78
[golgi:14384] [15] 17 nrniv 0x0000000100001aa8 start + 52
[golgi:14384] [16] 18 ??? 0x0000000000000007 0x0 + 7
[golgi:14384] *** End of error message ***
mpiexec noticed that job rank 0 with PID 14382 on node golgi.oist.jp exited on signal 15 (Terminated).
3 additional processes aborted (not shown)

I basically downloaded this model (http://senselab.med.yale.edu/modeldb/sh ... 7985&file=\) and ran sh modelfix.sh so that all the 3 models were in my modeldb folder. The fourth model in the same folder is the model on which I am working on. However i get this error for all the 4 models.

thanks,

shyam

[ted]

What version of NEURON are you using? (what is the first line of the "banner" message that appears in the xterm when NEURON starts?)

[shyam_u2]

Dear Ted,

I think its NEURON 7.1. Is that you want to know. When i click nrngui i get a white window which has the following lines.

-e
NEURON -- Release 7.1 (359:7f113b76a94b) 7f113b76a94b
Duke, Yale, and the BlueBrain Project -- Copyright 1984-2008
See http://www.neuron.yale.edu/credits.html

[ted]

That's what I needed to know.

With 7.2 (524:1a4443872b11) 2011-06-14, I was able to generate an mcomplex.dat file for the Miyasho et al. purkinje cell model, and then complete a multisplit simulation of that cell. Didn't have to modify the Hines et al. init.hoc at all.

I wonder if there's a bug in 7.1 that might be interfering. Can you uninstall NEURON, then install the latest alpha version and try again?

[shyam_u2]

Dear Ted,

For all the models (including mine) i was able to generate the mcomplex.dat file. But when i try to run using mpiexec it creates the error which i quoted before. Any way i will do what u said and contact you shortly.

Thanks.

[shyam_u2]

Dear Ted,

It works with NEURON 7.2. thank you.

Shyam

[ted]

Glad it worked.